Molecular divergence between disjunct taxa in eastern Asia and eastern North America

Eastern Asian-eastern North American disjuncts in four genera were examined for allozyme divergence and sequence divergence of the internal transcribed spacers (ITS) of nuclear ribosomal DNA. The disjunct pairs of taxa include Caulophyllum robustum-C. thalictroid.es, Menispermum dauricum-M. canadense, Penthorum chinense-P. sedoides, and Phryma leptostachya var. asiatica-P. leptostachya var. leptostachya. Allozyme divergence was comparable in Caulophyllum and Penthorum (genetic identities of 0.534 and 0.546) and was considerably higher than between pairs of taxa in Menispermum (0.273) and Phryma (0.291). Caulophyllum and Penthorum, which have the highest genetic identities at allozyme loci, also have low ITS sequence divergences (1.30 and 1.65%, respectively). Phryma, which has low isozyme identity, also has the highest ITS sequence divergence (4.46%). The two taxa of Menispermum have low ITS sequence divergence (0.93%) despite having a low identity (0.273) at allozyme loci. The results suggest that divergence between the taxa in the four genera are not the result of a single historical event. Estimated divergence times are reasonably consistent with a late Miocene disjunction for Caulophyllum and Penthorum, whereas the age of the Phryma disjunction is calculated at over 20 million years. The nonconcordant divergences between allozymes and ITS sequences in Menispermum may be caused by concerted evolution in the latter or possibly longer generation time in the woody plants. Additional molecular data are needed to clarify the situation.     

Phylogeny and biogeography of Sassafras (Lauraceae) disjunct between eastern Asia and eastern North America

Sassafras (Lauraceae) consists of three species disjunct between eastern Asia (S. tzumu and S. randaiense) and eastern North America (S. albidum). Phylogenetic analysis based on sequences of nuclear ribosomal ITS and three chloroplast non-coding regions (rpl16, trnL-F, and psbA-trnH) showed that Sassafras is monophyletic and that the eastern North American S. albidum is sister to the clade of its two eastern Asian counterparts. Their intercontinental divergence was estimated to be 13.80 ± 2.29−16.69 ± 2.52 million years ago (mya) using the penalized likelihood method with the ITS and three chloroplast markers. Biogeographic analyses combined with fossil evidence suggest that Sassafras has a relict distribution in the Northern Hemisphere without a Gondwanan link. The divergence time of the two eastern Asian species (the continental Chinese Sassafras tzumu and S. randaiense endemic to Taiwan) is estimated to be 0.61 ± 0.75−2.23 ± 0.76 mya. Sassafras randaiense from Taiwan was most likely derived from an ancestor from continental China.     

Molecular phylogeny and biogeography of Astilbe (Saxifragaceae) in Asia and eastern North America

Phylogenetic analyses were conducted for Astilbe (Saxifragaceae), an Asian/eastern North American disjunct genus, using sequences of nuclear ribosomal internal transcribed spacer (ITS) and plastid matK, trnL‐trnF and psbA‐trnH regions. The monophyly of Astilbe is well supported by both ITS and plastid sequences. Topological incongruence was detected between the plastid and the ITS trees, particularly concerning the placement of the single North American species, A. biternata, which may be most probably explained by its origin involving hybridization and/or allopolyploidy with plastid capture. In Astilbe, all species with hermaphroditic flowers constitute a well‐supported clade; dioecious species form a basal grade to the hermaphroditic clade. Astilbe was estimated to have split with Saxifragopsis from western North America at 20.69 Ma (95% HPD: 12.14–30.22 Ma) in the early Miocene. This intercontinental disjunction between Astilbe and Saxifragopsis most likely occurred via the Bering land bridge. The major clade of Astilbe (all species of the genus excluding A. platyphylla) was inferred to have a continental Asian origin. At least three subsequent migrations or dispersals were hypothesized to explain the expansion of Astilbe into North America, Japan and tropical Asian islands. The intercontinental disjunct lineage in Astilbe invokes a hybridization event either in eastern Asia or in North America. This disjunction in Astilbe may be explained by a Beringian migration around 3.54 Ma (95% high posterior density: 1.29–6.18 Ma) in the late Tertiary, although long‐distance dispersal from eastern Asia to North America is also likely. The biogeographical connection between continental Asia, Taiwan, the Philippines and other tropical Asian islands in Astilbe provides evidence for the close floristic affinity between temperate or alpine south‐western China and tropical Asia. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ●● , ●●–●●.     

Evolution of biogeographic disjunction between eastern Asia and eastern North America in Phryma (Phrymaceae)

This study examines molecular and morphological differentiation in Phryma L., which has only one species with a well-known classic intercontinental disjunct distribution between eastern Asia (EA) and eastern North America (ENA). Phylogenetic analysis of nuclear ribosomal ITS and chloroplast rps16 and trnL-F sequences revealed two highly distinct clades corresponding to EA and ENA. The divergence time between the intercontinental populations was estimated to be 3.68 ± 2.25 to 5.23 ± 1.37 million years ago (mya) based on combined chloroplast data using Bayesian and penalized likelihood methods. Phylogeographic and dispersal-vicariance (DIVA) analysis suggest a North American origin of Phryma and its migration into EA via the Bering land bridge. Multivariate analysis based on 23 quantitative morphological characters detected no geographic groups at the intercontinental level. The intercontinental populations of Phryma thus show distinct molecular divergence with little morphological differentiation. The discordance of the molecular and morphological patterns may be explained by morphological stasis due to ecological similarity in both continents. The divergence of Phryma from its close relatives in the Phrymaceae was estimated to be at least 32.32 ± 4.46 to 49.35 ± 3.18 mya.     

Molecular divergence in the eastern Asia– eastern North America disjunct section Rytidospermum of Magnolia (Magnoliaceae)

Molecular divergence in the eastern Asia—eastern North American disjunct section Rytidospermum of Magnolia was investigated by allozyme electrophoresis, chloroplast DNA (cpDNA) restriction site analysis, and gene sequencing. We calculated Nei's genetic identities between two Asian species, M. officinalis var. biloba and M. hypoleuca, and three American species, M. tripetala, M. fraseri var. fraseri, and M. macrophylla var. macrophylla, by using gene frequency data from 17 nuclear-encoded allozyme loci in 67 populations. We then estimated cpDNA sequence divergence between the five species by examining restriction site variation for ten endonucleases over the entire genome. Finally, nucleotide sequences of the chloroplast gene rbcL were compared between M. hypoleuca, M. tripetala, and M. macrophylla var. macrophylla. All three methods consistently yielded low divergence values between the American species M. tripetala and its Asian sister taxa, M. officinalis var. biloba and M. hypoleuca (Nei's I = 0.712 and 0.809, respectively; D-cpDNA = 0.083% for both pairs; D-rbcL = 0.000% between M. tripetala and M. hypoleuca). The other two American species, M. fraseri var. fraseri and M. macrophylla var. macrophylla, neither of which is sister to the Asian taxa, exhibited much higher divergence from the Asian taxa. We interpreted the low divergence between M. tripetala and its Asian sister taxa as a result of recent separation (the late Miocene to early Pliocene), based on time estimates from molecular data as well as geological and paleoclimatic evidence. A comparison of our results with those of the earlier studies revealed a diverse array of levels of divergence between several eastern Asian and eastern North American species pairs. Though different extinction patterns and variation in molecular evolutionary rates may be partly responsible, this heterogeneous pattern of divergence is best explained by different times of disjunction in different taxa, which in turn suggests that the floristic similarity between the two continents was most likely attained by multiple migrations via both Bering and North Atlantic land bridges, or possibly even with involvement of dispersal.     

Species richness in plant genera disjunct between temperate eastern Asia and North America

The species richness of 109 amphi-Pacific disjunct genera was examined in eastern Asia and North America. Although the entire flora of eastern Asia contains approximately one-third more species than that of North America, the difference in species richness among disjunct taxa is less. When woody and herbaceous genera are considered separately, the former exhibit a strong diversity bias favouring eastern Asia whereas there is no significant difference in diversity between continents among herbaceous genera. This result is not due to habitat differences between woody and herbaceous genera, because the disjunct herbs inhabit primarily moist forests and woodlands. This result is also not related to relative phylogenetic advancement, even though older major lineages of plants tend to have a predominance of woody taxa. Woody genera are distributed in lower latitudes than herbaceous genera on both continents, and both woody and herbaceous genera are distributed in lower latitudes in eastern Asia than in North America. The North American temperate flora is primarily a relict of a flora form 7 more widespread throughout the Northern Hemisphere. Contemporary patterns of diversity suggest that the effects of climate changes in the late Tertiary were less severe in eastern Asia and promoted diversification, but were more severe in North America and may have caused widespread extinction. The difference in the effect of climate change on diversity in herbaceous and woody lineages reflects the different ecological relationships of species having these contrasting life forms. Clearly, the contemporary floras of eastern Asia and North America bear the imprint of history and emphasize the important interface between ecological relationships and evolutionary responses.     

A cytological study on Kelloggia (Rubiaceae), an intercontinental disjunct genus between eastern Asia and western North America

A cytological study was carried out for the first time on four populations of the only two species of Kelloggia (Rubiaceae), which occur disjunctly in eastern Asia (K. chinensis Franch.) and western North America (K. galioides Torr.). The consistent mitotic prophase chromosome condensation pattern and interphase nuclei type were determined for both species. The chromosome base number of the genus is suggested to be x=11. The karyotype of 2n=22=2x=16m+6sm was examined for both species. The karyotypical asymmetry of 1A and 2A was found in K. chinensis and K. galioides, respectively. According to the predominant evolutionary direction of karyotype asymmetry in angiosperms, K. galioides (2A) seems slightly more evolved than K. chinensis (1A). Our finding is consistent with the hypothesis of the Old World origin of Kelloggia based on molecular study.     

Molecular phylogeny of treeshrews (Mammalia: Scandentia) and the timescale of diversification in Southeast Asia

Resolving the phylogeny of treeshrews (Order Scandentia) has historically proven difficult, in large part because of access to specimens and samples from critical taxa. We used "antique" DNA methods with non-destructive sampling of museum specimens to complete taxon sampling for the 20 currently recognized treeshrew species and to estimate their phylogeny and divergence times. Most divergence among extant species is estimated to have taken place within the past 20 million years, with deeper divergences between the two families (Ptilocercidae and Tupaiidae) and between Dendrogale and all other genera within Tupaiidae. All but one of the divergences between currently recognized species had occurred by 4Mya, suggesting that Miocene tectonics, volcanism, and geographic instability drove treeshrew diversification. These geologic processes may be associated with an increase in net diversification rate in the early Miocene. Most evolutionary relationships appear consistent with island-hopping or landbridge colonization between contiguous geographic areas, although there are exceptions in which extinction may play an important part. The single recent divergence is between Tupaia palawanensis and Tupaia moellendorffi, both endemic to the Philippines, and may be due to Pleistocene sea level fluctuations and post-landbridge isolation in allopatry. We provide a time-calibrated phylogenetic framework for answering evolutionary questions about treeshrews and about evolutionary patterns and processes in Euarchonta. We also propose subsuming the monotypic genus Urogale, a Philippine endemic, into Tupaia, thereby reducing the number of extant treeshrew genera from five to four.     

Molecular phylogeny of Juglans (Juglandaceae): a biogeographic perspective

The eastern Asian and eastern North American disjunction in Juglans offers an opportunity to estimate the time since divergence of the Eurasian and American lineages and to compare it with paleobotanical evidence. Five chloroplast DNA noncoding spacer (NCS) sequences: trnT−trnF, psbA−trnH, atpB−rbcL, trnV-16S rRNA, and trnS-trnfM and data from earlier studies (matK, ITS, and nuclear RFLP) were used to reconstruct phylogeny and to estimate the divergence time of major lineages. Seventeen taxa from four sections of Juglans and two outgroup taxa, Pterocarya stenoptera and Carya illinoiensis were included. NCS data was congruent only with matK data. Both maximum parsimony (MP) and maximum likelihood (ML) cladograms were concordant at the sectional level and revealed three well-supported monophyletic clades corresponding to sections Juglans, Cardiocaryon, and Rhysocaryon in both NCS and combined analyses. The single extant American butternut, Juglans cinerea was placed within the poorly resolved, but well-supported Rhysocaryon. Placement of taxa within Rhysocaryon and Cardiocaryon were inconsistent between NCS and combined analyses. Overall, the results suggest that: (1) the NCS sequence divergence observed within and between sections of Juglans is low and the addition of matK data only marginally improved resolution within Rhysocaryon; (2) the early divergence of section Juglans in both MP and ML analyses of NCS and combined data implies its ancient origin in contrast to fossil evidence, which suggests the earliest divergence of sections Rhysocaryon and Cardiocaryon; and (3) the extant taxa may not hold the footprints to unravel the evolutionary history of the genus.     

Polyphyly of the Padus group of Prunus (Rosaceae) and the evolution of biogeographic disjunctions between eastern Asia and eastern North America

Prunus subgenus Padus is a group with a wide distribution in temperate eastern Asia and eastern North America with one species extending to Europe and one to Central America. Phylogenetic relationships of subgenus Padus were reconstructed using sequences of nuclear ribosomal ITS, and plastid ndhF gene, and rps16 intron and rpl16 intron. Prunus subgenus Padus is shown to be polyphyletic. Taxa of subgenus Padus and subgenus Laurocerasus are highly intermixed in both the ITS and the plastid trees. The results support two disjunctions between eastern North America and Eurasia within the Padus group. One disjunction is between Prunus virginiana of eastern North America and P. padus of Eurasia, estimated to have diverged at 2.99 (95 % HPD 0.59–6.15)–4.1 (95 % HPD 0.63–8.59) mya. The other disjunction is between P. serotina and its Asian relatives. The second disjunction may have occurred earlier than the former one, but the age estimate is difficult due to the unresolved phylogenetic position of the P. serotina complex.     

Molecular phylogeny of the genus Vitis (Vitaceae) based on plastid markers

? Premise of the study: This work represents the first molecular phylogeny of the economically important genus Vitis, an important genetic resource for breeding in grapevine, Vitis vinifera. ? Methods: A molecular phylogeny of Vitis using a combined data set of three noncoding regions of the plastid DNA genome was constructed from 47 accessions covering 30 species of Vitis. The data for the trnL-F marker were combined with previously published data across the Vitaceae. ? Key results: The molecular phylogeny demonstrated monophyly of the genus Vitis. Based on the combined analysis of three genes, Vitis is split into three clades that mirror the continental distribution of these accessions. The diversity is highest in the Asian clade, but the general genetic distances across taxa from different continents are relatively small. ? Conclusions: The findings support a relatively recent and intense gene flow between East Asia and North America and the possible impact of hybridization on the evolution of the genus Vitis. Taxon identity in important stock collections should be screened carefully because roughly 10% of the accessions analyzed in the present study had been misidentified.     

A chloroplast phylogeny of Arisaema (Araceae) illustrates Tertiary floristic links between Asia, North America, and East Africa

The evolution of Arisaema is reconstructed, based on combined sequences (2048 aligned bases) from the chloroplast trnL intron, trnL-trnF spacer, and rpl20-rps12 spacer obtained for species from all 11 sections, including sectional type species and geographically disjunct East African and North American/Mexican species. Analyses were rooted with a representative sample of the closest outgroups, Pinellia and Typhonium, to rigorously test the monophyly of Arisaema. Sections in Arisaema are mostly based on leaf, stem, and inflorescence characters and, with one exception, are not rejected by the molecular data; however, statistical support for sectional relationships in the genus remains poor. Section Tortuosa, which includes eastern North American A. dracontium and Mexican A. macrospathum, is demonstrably polyphyletic. The third New World species, A. triphyllum, also occurs in eastern North America and groups with a different Asian clade than do A. dracontium/A. macrospathum. The genus thus appears to have entered North America twice. Fossil infructescences similar to those of A. triphyllum are known from approximately 18 million-year-old deposits in Washington State and can serve to calibrate a molecular clock. Constraining the age of A. triphyllum to 18 million years (my) and applying either a semiparametric or an ultrametric clock model to the combined data yields an age of approximately 31-49 my for the divergence of A. dracontium/A. macrospathum from their Asian relatives and of 19-32 my for the divergence between African A. schimperianum and a Tibetan/Nepalese relative. The genus thus provides an example of the Oligocene/Miocene floristic links between East Africa, Arabia, the Himalayan region, China, and North America. The phylogeny also suggests secondary loss of the environmental sex determination strategy that characterizes all arisaemas except for two subspecies of A. flavum, which have consistently bisexual spathes. These subspecies are tetraploid and capable of selfing, while a third subspecies of A. flavum is diploid and retains the sex-changing strategy. In the molecular trees, the sex-changing subspecies is sister to the two non-sex-changing ones, and the entire species is not basal in the genus.     

Molecular phylogeny and biogeographic history of the piculets (Piciformes: Picumninae)

The subfamily Picumninae (piculets) includes 3 genera and 30 species of tiny and short-tailed woodpeckers with a pantropical distribution. Within the Picumninae, two cases of intercontinentally disrupted distributions at the genus level occur. The first one concerns the genus Sasia (one species in Africa and two in southeast Asia) while the second concerns Picumnus (one species in southeast Asia and 25 in South America). These disrupted distributions, as well as several morphological differences, have lead some authors to place the African representative of Sasia and the southeast Asian representative of Picumnus in their own monotypic genera ( Verreauxia and Vivia , respectively). To address the taxonomic status and biogeographic history of the piculets, we sequenced 2676 bp of DNA from one mitochondrial (ND2) and two nuclear markers (myoglobin intron 2 and β-fibrinogen intron 7). Monophyly of Picumninae could not be recovered with confidence, while monophyly of Sasia and Picumnus were always strongly supported. Molecular dating analyses revealed that the splits both between the African and Indo-Malayan Sasia and between the New World and Old World Picumnus occurred at ca 7.9 Myr BP. This time corresponds to the beginning of the formation of the northern Hemisphere ice sheets and the accompanying expansion of grasslands throughout the world. The spread of open areas in the northern parts of Eurasia and America prevented gene flow between tropical forest birds, such as the piculets, in Africa, southeast Asia and South America, respectively.     

Molecular phylogeny and diversification history of Prosopis (Fabaceae: Mimosoideae)

The genus Prosopis is an important member of arid and semiarid environments around the world. To study Prosopis diversification and evolution, a combined approach including molecular phylogeny, molecular dating, and character optimization analysis was applied. Phylogenetic relationships were inferred from five different molecular markers ( mat K- trn K, trn L- trn F, trn S- psb C, G3pdh, NIA). Taxon sampling involved a total of 30 Prosopis species that represented all Sections and Series and the complete geographical range of the genus. The results suggest that Prosopis is not a natural group. Molecular dating analysis indicates that the divergence between Section Strombocarpa and Section Algarobia plus Section Monilicarpa occurred in the Oligocene, contrasting with a much recent diversification (Late Miocene) within each of these groups. The diversification of the group formed by species of Series Chilenses, Pallidae, and Ruscifoliae is inferred to have started in the Pliocene, showing a high diversification rate. The moment of diversification within the major lineages of American species of Prosopis is coincident with the spreading of arid areas in the Americas, suggesting a climatic control for diversification of the group. Optimization of habitat parameters suggests an ancient occupation of arid environments by Prosopis species.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 621–640.     

Genetic variation and biogeography of the disjunct Vitis subg. Vitis (Vitaceae)

Aim Vitis subg. Vitis provides an example of a plant disjunction occurring in the Northern Hemisphere. It shows broad morphological variation but is assumed to be a species complex with limited genetic differentiation. Based on a comprehensive sampling of taxa and polymorphism in both chloroplast and nuclear DNA, we assessed genetic variation within this subgenus. Our aims were to clarify the relationships among species and to examine their historical biogeography. Location Asia, Europe, North America. Methods We analysed a total of 30 species and putative hybrids from subgenus Vitis and examined the infra‐specific variation in some species. Polymorphism in chloroplast DNA was assessed in trnL and trnH–psbA–trnK sequences (c. 2170 bp) and in 15 microsatellite loci. We also obtained nuclear data for size variation at 24 microsatellite loci. Phylogenetic inference was performed with Bayesian analyses. A maximum parsimony network was constructed to depict the evolutionary relationships among haplotypes, and microsatellite data were also subjected to hierarchical clustering analysis using the Ward distance. In addition, we assessed size homoplasy by sequencing both chloroplast and nuclear microsatellite loci. Results Chloroplast polymorphisms resolved subgenus Vitis as a monophyletic group with limited genetic variation. The ancestral haplotypes were found in Eurasia. American taxa all harboured derived haplotypes. Most of them formed a monophyletic group that did not include Vitis californica. The four main haplotypes in Vitis vinifera corresponded to two different origins. Nuclear microsatellites indicated that genetic variation was especially large in North America. Asian species exhibited a lower level of nuclear divergence and the European V. vinifera corresponded to a differentiated nuclear lineage. Main conclusions We obtained some evidence that subgenus Vitis has an Asian origin and then dispersed to Europe and North America. Geographic separation was followed by diversification, presumably during the Pleistocene, resulting in phylogeographic patterns similar to other biota. In contrast to chloroplast DNA, nuclear DNA shows a larger than expected genetic variation. Our molecular data also highlight the need to re‐examine certain aspects of the current subgeneric classification.     

东亚——北美东部间断透骨草属的扩增片段长度多态性

透骨草属(Phryma)是一个单种属,间断分布于东亚与北美东部.尽管东亚与北美东部居群形态差异非常小,但分子变异却非常明显.本研究进一步运用AFLP两对引物来衡量透骨草属的遗传多样性并评估其形态保守性.结果发现透骨草的遗传差异主要存在于两大洲的居群之间.聚类与PCA分析显示透骨草分成两大支与其地理分布相吻合,一支全部来自东亚,另一支则是北美东部的居群.我们的结果强烈支持透骨草东亚--北美东部居群存在明显的遗传分化和形态保守.     

A combined morphological and molecular phylogenetic analysis of Parthenocissus (Vitaceae) and taxonomic implications

Parthenocissus (the Virginia creeper genus, Vitaceae) consists of 13 species and shows a disjunct distribution between Asia and North America. We investigated the inflorescence structure, calyx morphology, appendages on the inner side of petals, leaf epidermis, pollen and seed characters throughout the genus. A combined phylogenetic analysis with 27 morphological and 4137 molecular characters was conducted and the result was largely congruent with that of the previous molecular work, but with higher resolution. The combined analysis identified two clades corresponding to the Asian and North American taxa. Parthenocissus feddei was resolved as closely related to the clade containing P. cuspidifera, P. heterophylla and P. semicordata. The four species share synapomorphies of having conspicuously raised veinlets, an obscurely five‐ (to eight‐) lobed calyx, appendages on the inner side of petals covering the entire length of anthers and foveolate pollen exine ornamentation. Within the Old World clade, the pentafoliolate species were weakly supported as more closely related to species with both simple and trifoliolate leaves. Furthermore, the ancestral states of tendril apices, inflorescence structure, appendages on the inner side of petals and exine ornamentation of pollen grains were reconstructed on the molecular strict consensus tree. The appendages on the inner side of petals and exine ornamentation of pollen grains were suggested to be important characters in the taxonomy of Parthenocissus, especially for species with trifoliolate leaves. Finally, the previous classifications of Parthenocissus were evaluated within the phylogenetic framework. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, ?? , ??–??.     

Molecular phylogeny of Mentawai macaques: taxonomic and biogeographic implications

In order to elucidate the evolutionary history and taxonomy of the Mentawai macaques, we sequenced a 567 base pairs (bp) long fragment of the mitochondrial cytochrome b gene from 39 individuals representing pigtailed macaque populations from Siberut, Sipora, South Pagai, and Sumatra. Pairwise difference analyses carried out within and among populations have shown, that: (1) variation within populations is relative low, (2) variation among populations is increased, and (3) pairwise differences within and among the populations from Sipora and South Pagai are in the same range. From phylogenetic tree reconstructions including further macaque species, we detected a paraphyletic origin of Mentawai macaques with the Siberut population more closely related to Macaca nemestrina from Sumatra, than it is to populations from the Southern islands. Based on these results, we favour a scenario in that macaques entered the Mentawai islands by two independent colonisation events. Taking together the paraphyletic origin of Mentawai macaques and the genetic differences detected among pigtailed macaque populations, which are comparable with those observed among the seven Sulawesi macaque species, we propose to separate macaques from Siberut and Sipora, North and South Pagai into two distinct species, Macaca siberu and Macaca pagensis, respectively.